Alterations in fecal microbiota and inflammatory biomarkers in goats with Mycobacterium avium subsp. paratuberculosis infection

Johne’s disease (JD) is a form of chronic enteritis in ruminants that results in significant economic losses in the livestock industry. Previous studies in cattle have compared Mycobacterium avium subsp. paratuberculosis (MAP)-positive and MAP-negative animals but did not characterize microbial changes across distinct infection groups, while microbiome studies on caprine paratuberculosis remain limited. Therefore, this study aimed to investigate alterations in fecal microbiota and inflammatory biomarkers in goats classified into MAP infection groups. MAP infection was associated with reduced microbial richness and significant alterations in community composition among groups. Infectious goats showed lower Shannon and Gini–Simpson diversity indices and apparent separation in beta-diversity analysis, which was accompanied by greater within-group dispersion. At the phylum level, Actinobacteria was more abundant in infected goats, while Proteobacteria exceeded the 1% threshold only in infectious goats; Fibrobacteres, Spirochaetes, and Verrucomicrobia did not exceed the 1% relative abundance threshold. Linear discriminant analysis effect size analysis identified 48 discriminative taxa across taxonomic ranks, of which 28 (58.3%) were also identified as significant by Analysis of Compositions of Microbiomes with Bias Correction 2. Pairwise comparisons showed that most genera with higher relative abundances in control and infected goats did not differ between the two groups but showed significantly lower relative abundance in the infectious goats. Mediterraneibacter was the only genus that differed between the control and infectious groups, with a higher relative abundance in the infectious group in both analyses. Among inflammatory biomarkers, fecal calprotectin was significantly elevated in the infectious goats, whereas serum leucine-rich α-2 glycoprotein and S100A12 levels were reduced in MAP-infected animals. C-reactive protein levels did not differ significantly among groups. Exploratory Spearman’s correlation analysis revealed significant associations between genus-level microbiota and inflammatory biomarkers. Goats with MAP infection showed group-level differences in microbial diversity and composition, with the most pronounced differences observed in goats with detectable fecal MAP shedding. Inflammatory biomarkers showed distinct group-level profiles that complemented the microbial findings. These results provide a basis for understanding host–microbiome interactions during JD in goats.